HPO annotations distribution

HP Patient percentage
Abdominal aortic aneurysm 5.0
Cryptorchidism 20.0
Hydroureter 5.0
Hydronephrosis 10.0
Xerostomia 5.0
Pectus excavatum 5.0
Pectus carinatum 10.0
Congenital hip dislocation 5.0
Oligohydramnios 5.0
Patent ductus arteriosus 5.0
Talipes equinovarus 10.0
Anal atresia 5.0
Prune belly 5.0
Aplasia of the abdominal wall musculature 5.0
Congenital posterior urethral valve 5.0
Slow pupillary light response 5.0
Strabismus 25.0
Abducens palsy 5.0
Cleft palate 20.0
Cleft upper lip 5.0
Microcephaly 10.0
Esotropia 5.0
Microphthalmia 5.0
Hypertension 5.0
Cutis marmorata 5.0
Brachydactyly 25.0
Intellectual disability 25.0
Seizure 10.0
Global developmental delay 5.0
Generalized hypotonia 5.0
Pachygyria 5.0
Calvarial skull defect 5.0
Alopecia 5.0
Ventricular septal defect 10.0
Atrial septal defect 5.0
Tetralogy of Fallot 5.0
Pulmonic stenosis 5.0
Bicuspid aortic valve 5.0
Aortic valve stenosis 5.0
Toe syndactyly 10.0
Small nail 5.0
Hypoplasia of the corpus callosum 10.0
Encephalocele 5.0
Pulmonary arterial hypertension 5.0
Ventriculomegaly 10.0
Polymicrogyria 5.0
Cortical dysplasia 5.0
Supernumerary nipple 5.0
Hypoplastic left heart 5.0
Pulmonary artery stenosis 5.0
Periventricular leukomalacia 5.0
Aplasia cutis congenita on trunk or limbs 5.0
Aplasia cutis congenita over posterior parietal area 5.0
Imperforate hymen 5.0
Acanthosis nigricans 5.0
Brachycephaly 15.0
Micrognathia 15.0
Arachnodactyly 5.0
Joint hypermobility 10.0
Broad skull 5.0
Hydrocephalus 20.0
Macrocephaly 5.0
Malar flattening 20.0
Recurrent otitis media 5.0
Conductive hearing impairment 5.0
Choanal stenosis 15.0
Short ribs 5.0
Motor delay 5.0
Megalencephaly 10.0
Limited elbow extension 5.0
Polyhydramnios 10.0
Premature rupture of membranes 5.0
Frontal bossing 10.0
Pulmonary hypoplasia 5.0
Respiratory distress 5.0
Brain stem compression 5.0
Small foramen magnum 5.0
Generalized joint hypermobility 5.0
Upper airway obstruction 5.0
Lumbar hyperlordosis 5.0
Genu varum 5.0
Femoral bowing 5.0
Radial bowing 5.0
Flared metaphysis 5.0
Ulnar bowing 5.0
Limited hip extension 5.0
Short femur 5.0
Narrow greater sciatic notch 5.0
Trident hand 5.0
Severe platyspondyly 5.0
Thoracic hypoplasia 5.0
Depressed nasal bridge 20.0
Spinal stenosis with reduced interpedicular distance 5.0
Lumbar kyphosis in infancy 5.0
Narrow vertebral interpedicular distance 10.0
Rhizomelia 5.0
Neonatal short-limb short stature 5.0
Floppy infant 5.0
Midface retrusion 15.0
Feeding difficulties 5.0
Short femoral neck 5.0
Paroxysmal sneezing 5.0
Tinnitus 5.0
Hearing impairment 20.0
Visual loss 5.0
Diplopia 5.0
Personality changes 5.0
Cafe-au-lait spot 5.0
Axillary freckling 5.0
Neurofibroma 5.0
Ataxia 5.0
Headache 5.0
Vertigo 5.0
Ependymoma 5.0
Juvenile posterior subcapsular lenticular opacities 5.0
Bilateral vestibular schwannoma 5.0
Unilateral vestibular schwannoma 5.0
Astrocytoma 5.0
Peripheral schwannoma 5.0
Retinal hamartoma 5.0
Lisch nodules 5.0
Peripheral neuropathy 5.0
Inguinal freckling 5.0
Epiretinal membrane 5.0
Cortical cataract 5.0
Optic nerve sheath meningioma 5.0
Vaginal atresia 5.0
Narrow palate 10.0
Bifid uvula 5.0
High palate 10.0
Thin upper lip vermilion 5.0
Large fontanelles 5.0
Brachyturricephaly 10.0
Delayed cranial suture closure 10.0
Mandibular prognathia 20.0
Hypertelorism 20.0
Broad forehead 5.0
High forehead 10.0
Posteriorly rotated ears 5.0
Low-set ears 10.0
Chronic otitis media 5.0
Choanal atresia 10.0
Anteverted nares 10.0
Downslanted palpebral fissures 15.0
Myopia 5.0
Shallow orbits 15.0
Delayed eruption of teeth 10.0
Dental malocclusion 10.0
Hyperhidrosis 5.0
Acne 5.0
Postaxial hand polydactyly 5.0
Preaxial hand polydactyly 5.0
Agenesis of corpus callosum 5.0
Cerebellar hypoplasia 5.0
Absent septum pellucidum 5.0
Pyloric stenosis 5.0
Esophageal atresia 5.0
Overriding aorta 5.0
Delayed epiphyseal ossification 5.0
Limited elbow movement 5.0
Humeroradial synostosis 10.0
Ectopic anus 5.0
Coronal craniosynostosis 15.0
Sagittal craniosynostosis 5.0
Lambdoidal craniosynostosis 10.0
Anomalous tracheal cartilage 5.0
Acrobrachycephaly 5.0
Cervical C5/C6 vertebrae fusion 5.0
Rhizomelic arm shortening 5.0
Synostosis of carpal bones 5.0
Wide intermamillary distance 5.0
Chiari type I malformation 5.0
Posterior fossa cyst 5.0
Abnormal morphology of the limbic system 5.0
Broad distal hallux 5.0
Broad distal phalanx of the thumb 5.0
Cutaneous finger syndactyly 5.0
Cutaneous syndactyly of toes 5.0
Prominent forehead 5.0
Flat face 10.0
Arachnoid cyst 5.0
Oxycephaly 5.0
Low anterior hairline 5.0
Facial asymmetry 5.0
Hypoplasia of the maxilla 15.0
Convex nasal ridge 5.0
Narrow nose 5.0
Ptosis 5.0
Buphthalmos 5.0
Abnormal nasolacrimal system morphology 5.0
Plagiocephaly 5.0
Abnormal heart morphology 5.0
Hallux valgus 5.0
Intellectual disability, moderate 5.0
Abnormal pelvic girdle bone morphology 5.0
Skull asymmetry 5.0
Parietal foramina 5.0
Radioulnar synostosis 5.0
Breast carcinoma 5.0
Long nose 5.0
Clinodactyly of the 5th finger 5.0
Short stature 10.0
Flat forehead 5.0
Microtia 5.0
Prominent crus of helix 5.0
Partial duplication of the distal phalanx of the 2nd finger 5.0
Partial duplication of the distal phalanx of the 3rd finger 5.0
Absent first metatarsal 5.0
Cleft of chin 5.0
Dental crowding 5.0
Chiari malformation 5.0
Cloverleaf skull 5.0
Bronchomalacia 5.0
Elbow ankylosis 5.0
Short nose 5.0
Short middle phalanx of toe 5.0
Tracheal cartilaginous sleeve 5.0
Finger syndactyly 5.0
Shortening of all middle phalanges of the fingers 5.0
Broad hallux 5.0
Broad thumb 5.0
3-4 toe cutaneous syndactyly 5.0
Unilateral renal agenesis 5.0
Hypogonadism 5.0
Epicanthus 5.0
Broad nasal tip 5.0
Blue irides 5.0
Optic atrophy 5.0
Hypodontia 5.0
Congenital hypothyroidism 5.0
Irregular menstruation 5.0
Melanocytic nevus 5.0
Broad palm 5.0
Intrauterine growth retardation 10.0
Small for gestational age 5.0
Mild postnatal growth retardation 5.0
Long hallux 5.0
Scoliosis 5.0
Hyperphosphatemia 5.0
Elevated circulating thyroid-stimulating hormone concentration 5.0
Dislocated radial head 5.0
Elevated circulating parathyroid hormone level 5.0
Spinal canal stenosis 5.0
Elevated circulating calcitonin concentration 5.0
Short palm 10.0
Calvarial hyperostosis 5.0
Accelerated skeletal maturation 5.0
Neonatal epiphyseal stippling 5.0
Hypoplastic vertebral bodies 5.0
Disproportionate short-limb short stature 5.0
Short phalanx of finger 5.0
Short metacarpal 5.0
Cone-shaped epiphyses of the phalanges of the hand 5.0
Short metatarsal 5.0
Mild global developmental delay 5.0
Decreased growth hormone responses to growth hormone-releasing hormone challenge 5.0
Hypospadias 5.0
Widow's peak 5.0
Prominent nose 5.0
Webbed neck 5.0
Carious teeth 5.0
Single transverse palmar crease 5.0
Cerebellar vermis hypoplasia 5.0
Cerebral cortical atrophy 5.0
Enlarged cisterna magna 5.0
Spina bifida occulta 5.0
Preauricular pit 5.0
Mandibulofacial dysostosis 5.0
Fine hair 5.0
Allergy 5.0
Papule 5.0
Skin plaque 5.0
Hyperkeratosis 5.0
Acrokeratosis 10.0
Ridged nail 5.0
Punctate palmoplantar hyperkeratosis 5.0
Verrucous papule 5.0
Epidermal acanthosis 5.0
Acantholysis 5.0
Symmetric great toe depigmentation 5.0
Tall stature 5.0
Abnormality of the eye 5.0
Soft skin 5.0
Large hands 10.0
Long foot 5.0
Cutis gyrata of scalp 5.0
Periostosis 5.0
Sloping forehead 5.0
Bulbous nose 5.0
Telecanthus 5.0
Blepharophimosis 5.0
Synophrys 5.0
Tapered finger 5.0
Specific learning disability 5.0
Large for gestational age 5.0
Deep philtrum 5.0
Highly arched eyebrow 5.0
Thickened calvaria 5.0
Thick nasal alae 5.0
Short 5th metacarpal 5.0
Thick vermilion border 5.0

Ontoplot. Different calls examples (Click me)

Static ontoplot, frequency by size, guide lines set by ontology term points. Without propagating parent terms in frequencies
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "static", freq_by="size", fix_alpha="none", guide_lines="ont", count_parentals=False)

Static ontoplot, frequency by size, guide lines set by ontology term points. Propagating parent terms in frequencies
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "static", freq_by="size", fix_alpha="none", guide_lines="ont", count_parentals=True)

Static ontoplot, frequency by size, guide lines set by ontology term points. Propagating parent terms in frequencies. Minimum frequency threshold of 0.2
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "static", freq_by="size", fix_alpha="none", guide_lines="ont", count_parentals=True, onto_min_freq=0.2)

Dynamic ontoplot, frequency by size and opacity, opacity low values fixed by cubic root, guide lines set by ontology term points
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "dynamic", freq_by="both", fix_alpha="cubic_root", guide_lines="ont", count_parentals=True)

Dynamic ontoplot, frequency by size, guide lines set by concentric lines at each level of the ontology
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "dynamic", freq_by="size", fix_alpha="none", guide_lines="grid", count_parentals=True)

Dynamic ontoplot, frequency by opacity, no guide lines used
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "dynamic", freq_by="alpha", fix_alpha="none", guide_lines="none", count_parentals=True)

Static ontoplot, frequency by size and opacity, opacity low values fixed by cubic root, guide lines set by ontology term points
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "static", freq_by="both", fix_alpha="bins", guide_lines="ont", count_parentals=True)

Static ontoplot, frequency by size, guide lines set by concentric lines at each level of the ontology
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "static", freq_by="size", fix_alpha="none", guide_lines="grid", count_parentals=True)

Static ontoplot, frequency by opacity, no guide lines used
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "static", freq_by="alpha", fix_alpha=lambda x: x**(1/3), guide_lines="none", count_parentals=True)

Dynamic ontoplot centered in HP:0012443 (Abnormal brain morphology), using childs of HP:0012443 as main branches colors, frequency by size and opacity, opacity low values fixed by cubic root, guide lines set by ontology term points
plotter.ontoplot(ontology="ontology", root_node="HP:0012443", reference_node="HP:0012443", dpi = 300, height=800, width=800, title=f"Profiles signature", mode = "dynamic", freq_by="both", fix_alpha="cubic_root", guide_lines="ont", count_parentals=True)

Canvasxpress ontoplot, frequency by size (only mode), guide lines set by ontology term points
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=700, width=1400, title=f"Profiles signature", mode = "canvas", freq_by="size", fix_alpha="none", guide_lines="ont", count_parentals=True)


Canvasxpress ontoplot, frequency by size (only mode), guide lines set by concentric lines at each level of the ontology
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=700, width=1400, title=f"Profiles signature", mode = "canvas", freq_by="size", fix_alpha="none", guide_lines="grid", count_parentals=True)


Canvasxpress ontoplot. Adding a config as an argument to change any canvas configuration parameter
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=700, width=1400, title=f"Profiles signature", mode = "canvas", freq_by="size", fix_alpha="none", guide_lines="grid", config={"sizeStep": 5}, count_parentals=True)


Dynamic ontoplot. Defining custom configuration and layout or polar layout for plotly (dict can also be expressed as {} form) and point sizes (base size and scaling factors to frequency)
plotter.ontoplot(ontology="ontology", root_node="HP:0000118", reference_node="HP:0000118", dpi = 300, height=1800, width=2400, title=f"Profiles signature", mode = "dynamic", freq_by="both", fix_alpha="none", guide_lines="ont", plotly_layout=dict(legend=dict(font=dict(size=24)), polar=dict(radialaxis=dict(tickfont=dict(size=24)))), config={'toImageButtonOptions': {'format': 'png', 'height': 1800, 'width': 2400, 'scale': 5}}, user_sizes={'ont_size': 3, 'prof_base_size': 5, 'prof_size_factor': 40}, count_parentals=True)